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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataattccgcaaccatttatgtaataatggtgttgattaatctgaaaggtgaaatggagattttgtaattaacaacttactctcgagtgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGAAGCAAGATGTCTACACAGACATCTGCTCCACAAATTTCCGATGTATAGC

Basic information

species Oryza sativa
transcript LOC_Os11g01439.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 5
------------------gtatataattccgcaaccatttatgt-aataat---ggtgttgattaatctgaaaggtgaaatggagattttgtaattaacaacttactctcgagtgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGAAGCAAGATGTCTACACAGACATCTGCTCCACAAATTTCCGATGTATAGC
                  || |  |       ||    | | |  |||| |    |     |   |  | | |||||| ||| | |||| | ||| |  |||||| ||        |||||||||||| || || || ||||  ||||||||||| || ||||||||||||||||||||||||  |||||| | |||||||||||| || || || |  |   
gtgtgaggttctctttccgtgttcatcaggtaaaatcctcacgccaatattttcagaacccaggtacttcacaggtgatatgaatatttcg-aatcagtaacttattcatctaccttctgcagTTTGCTGGGGGATTTGATGCAGAAAGCATGAAAGCTTTTGAAGAGCTAAGAAGCAAGATGAGTACACATAAATCTGCTCCACAGATATCTGAAGGCTGA-
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29630415|gb|CB635424.1|CB635424
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|58695568|gb|CK084255.1|CK084255
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|29646000|gb|CB651007.1|CB651007
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86881810|gb|CI324099.1|CI324099
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|18386571|gb|BM419769.1|BM419769
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86832395|gb|CI315130.1|CI315130
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|15856550|gb|BI809362.1|BI809362
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGCCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|29612706|gb|CB617719.1|CB617719
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86887111|gb|CI325926.1|CI325926
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|27547352|gb|CA765429.2|CA765429
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|29612723|gb|CB617736.1|CB617736
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86597114|gb|CI272709.1|CI272709
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|29613986|gb|CB618999.1|CB618999
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86833430|gb|CI336219.1|CI336219
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTCCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|18387726|gb|BM420924.1|BM420924
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|15858456|gb|BI811268.1|BI811268
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|29668095|gb|CB664370.1|CB664370
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|29632488|gb|CB637497.1|CB637497
EST:     GAGAGTTCTTGTTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|58609462|gb|CK037495.1|CK037495
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCAT
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCAT
EST: gi|86866410|gb|CI343399.1|CI343399
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|29629417|gb|CB634426.1|CB634426
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86864001|gb|CI332927.1|CI332927
EST:     GAGAGTTCTTGCTTCTTCAGGTTTTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86893099|gb|CI333401.1|CI333401
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
EST: gi|86845832|gb|CI347092.1|CI347092
EST:     GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAG                         TTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA
genomic: GAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 47 (downstream exon)
Score: 114

GGTTGCCACAGAGCTTGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGTTCTTGCTTCTTCAGGGTGTGAGATTTGCTTTCCGAGTTCATCAGgtatataatt ... tgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGAAGCAAGATGTCTACACAGACATCTGCTCCACAAATTTCCGATGTATAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaggtgaaatggagattttgtaattaacaacttactctcgagtgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGAAGCAAGATGTCTACACAGACATCTGCTCCACAAATTTCCGATGTATAGC
                               aacttac  putative branch site (score: 114)
                 attttgtaattaacaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataattccgcaaccatttatgtaataatggtgttgattaatctgaaaggtgaaatggagattttgtaattaacaacttactctcgagtgctctgcagTTTGCCGGAGGGTTCGATGAGGAAAGCATGAAGGCATTTGAAGAGCTAAGAAGCAAGATGTCTACACAGACATCTGCTCCACAAATTTCCGATGTATAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG